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Headley SA, Dall Agnol AM, Alfieri AF, Alfieri AA, Buczinski S. The effects of simultaneous respiratory infections on the nasal shedding of Mycoplasmopsis bovirhinis in dairy calves. Vet Res Commun 2024:10.1007/s11259-024-10529-3. [PMID: 39287894 DOI: 10.1007/s11259-024-10529-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 09/01/2024] [Indexed: 09/19/2024]
Abstract
Although there are several studies that described the possible participation of Mycoplasmopsis bovirhinis (formerly, Mycoplasma bovirhinis) in respiratory disease in calves worldwide, none of these evaluated the effects of concomitant infections on the shedding of this organism. Accordingly, this study evaluated the effects of simultaneous respiratory infections in dairy calves on the nasal shedding of M. bovirhinis. A statistical two-step model, using univariable and multivariable with logistic regression was developed to investigate and predict the possible effects of simultaneous infections by Histophilus somni, Mannheimia haemolytica, Pasteurella multocida, bovine coronavirus (BCoV), and ovine gammaherpesvirus 2 (OvGHV2) in dairy calves on the nasal shedding of M. bovirhinis. The multivariable analysis demonstrated that dairy calves infected with OvGHV2 have 2.59 times likelihood of nasal shedding of M. bovirhinis relative to calves not infected by OvGHV2, while the odds of nasal shedding of M. bovirhinis was 3.46 times higher in dairy calves infected by M. haemolytica. In contrast, simultaneous respiratory infections in dairy calves by H. somni, P. multocida, and BCoV had no direct effect on the nasal shedding of M. bovirhinis. Consequently, infections by OvGHV2 and M. haemolytica may be possible risk factors for the nasal shedding of M. bovirhinis in dairy calves. These results demonstrated the importance of disease modeling in veterinary medicine to predict and understand the complex outcomes of associations in animals concomitantly infected by several disease pathogens.
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Affiliation(s)
- Selwyn Arlington Headley
- Laboratory of Animal Pathology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário, Londrina, Paraná, 86057-970, Brazil.
- Multi-User Animal Health Laboratory (LAMSA), Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Paraná, Brazil.
- National Institute of Science and Technology for Dairy Production Chain (INCT-LEITE), Universidade Estadual de Londrina, Londrina, Brazil.
| | - Alais Maria Dall Agnol
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Paraná, Brazil
| | - Alice Fernandes Alfieri
- Multi-User Animal Health Laboratory (LAMSA), Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Paraná, Brazil
- National Institute of Science and Technology for Dairy Production Chain (INCT-LEITE), Universidade Estadual de Londrina, Londrina, Brazil
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Paraná, Brazil
| | - Amauri Alcindo Alfieri
- Multi-User Animal Health Laboratory (LAMSA), Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Paraná, Brazil
- National Institute of Science and Technology for Dairy Production Chain (INCT-LEITE), Universidade Estadual de Londrina, Londrina, Brazil
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Paraná, Brazil
| | - Sébastien Buczinski
- Département des Sciences Cliniques, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
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Chen Y, Jia X, Gao Y, Ren X, Du B, Zhao H, Feng Y, Xue G, Cui J, Gan L, Feng J, Fan Z, Fu T, Xu Z, Yu Z, Yang Y, Zhao S, Huang L, Ke Y, Cao L, Yan C, Yuan J. Increased macrolide resistance rate of Mycoplasma pneumoniae correlated with epidemic in Beijing, China in 2023. Front Microbiol 2024; 15:1449511. [PMID: 39171272 PMCID: PMC11337199 DOI: 10.3389/fmicb.2024.1449511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 07/22/2024] [Indexed: 08/23/2024] Open
Abstract
We collected respiratory specimens from 128 pediatric patients diagnosed with pneumonia in Beijing in late 2023. Mycoplasma pneumoniae was detected in 77.3% (99/128) patients, with 36.4% (4/11), 82.9% (34/41), 80.3% (61/76) in children aged less than 3 years, 3-6 years, over 7 years, respectively. Mycoplasma pneumoniae (M. pneumoniae) was characterized using P1 gene typing, MLVA typing and sequencing of domain V of the 23S rRNA gene. P1 gene type 1 (P1-1; 76.1%, 54/71) and MLVA type 4-5-7-2 (73.7%, 73/99) were predominant. MLVA identified a new genotype: 3-4-6-2. Macrolide resistance-associated mutations were detected in 100% of samples, with A2063G accounting for 99% and A2064G for 1%. The positive rate of M. pneumoniae was higher compared to previous reports, especially in children less than 3 years, suggesting a M. pneumoniae epidemic showing a younger age trend occurred in late 2023 in Beijing, China. Higher proportions of macrolide-resistant M. pneumoniae, P1-1 and 4-5-7-2 genotype M. pneumoniae indicated increased macrolide resistance rate and genotyping shift phenomenon, which might be attributable to this epidemic. Additionally, complete clinical information from 73 M. pneumoniae pneumonia inpatients were analyzed. The incidence of severe M. pneumoniae pneumonia was 56.2% (41/73). Mycoplasma pneumoniae pneumonia patients exhibited longer duration of fever, with a median value of 10.0 days (IQR, 8.0-13.0), and higher incidence of complications (74.0%, 54/73). However, in this cohort, we found that the severity of M. pneumoniae pneumonia, co-infection, or complications were not associated with M. pneumoniae P1 gene or MLVA types. Clinicians should be aware that patients infected with macrolide-resistant M. pneumoniae exhibited more severe clinical presentations.
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Affiliation(s)
- Yujie Chen
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Xinyu Jia
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yagang Gao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Xue Ren
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Bing Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Hanqing Zhao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yanling Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Guanhua Xue
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jinghua Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Lin Gan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Junxia Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zheng Fan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Tongtong Fu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziying Xu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zihui Yu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yang Yang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shuo Zhao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Lijuan Huang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yuehua Ke
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ling Cao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jing Yuan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
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Arendt M, Stadler J, Ritzmann M, Ade J, Hoelzle K, Hoelzle LE. Hemotrophic Mycoplasmas-Vector Transmission in Livestock. Microorganisms 2024; 12:1278. [PMID: 39065047 PMCID: PMC11279228 DOI: 10.3390/microorganisms12071278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Hemotrophic mycoplasmas (HMs) are highly host-adapted and specialized pathogens infecting a wide range of mammals including farm animals, i.e., pigs, cattle, sheep, and goats. Although HMs have been known for over 90 years, we still do not know much about the natural transmission routes within herds. Recently, it has been repeatedly discussed in publications that arthropod vectors may play a role in the transmission of HMs from animal to animal. This is mainly since several HM species could be detected in different potential arthropod vectors by PCR. This review summarizes the available literature about the transmission of bovine, porcine, ovine, and caprine HM species by different hematophagous arthropod vectors. Since most studies are only based on the detection of HMs in potential vectors, there are rare data about the actual vector competence of arthropods. Furthermore, there is a need for additional studies to investigate, whether there are biological vectors in which HMs can multiply and be delivered to new hosts.
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Affiliation(s)
- Mareike Arendt
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany; (M.A.); (J.A.); (K.H.)
| | - Julia Stadler
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany; (J.S.); (M.R.)
| | - Mathias Ritzmann
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany; (J.S.); (M.R.)
| | - Julia Ade
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany; (M.A.); (J.A.); (K.H.)
| | - Katharina Hoelzle
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany; (M.A.); (J.A.); (K.H.)
| | - Ludwig E. Hoelzle
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany; (M.A.); (J.A.); (K.H.)
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Ade J, Eddicks M, Ritzmann M, Hoelzle K, Hoelzle LE, Stadler J. Haemotrophic Mycoplasmas Infecting Pigs: A Review of the Current Knowledge. Microorganisms 2024; 12:1267. [PMID: 39065036 PMCID: PMC11279051 DOI: 10.3390/microorganisms12071267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 07/28/2024] Open
Abstract
Haemotrophic mycoplasmas (haemoplasmas) are a group of highly specific and adapted bacteria. Three different haemoplasma species in pigs are known to date: Mycoplasma (M.) suis, M. parvum and 'Candidatus (Ca.) M. haemosuis'. Even though these bacteria have been known in pig farming for a long time, it is difficult to draw general conclusions about the relevance of their infections in pigs. This review summarizes the current knowledge on the three porcine haemoplasma species with regards to clinical and pathological descriptions, pathobiology, epidemiology and diagnostics as well as prevention and therapy. Overall, it is clear that considerably more data are available for M. suis than for the other two species, but generally, porcine haemoplasmas were found to be highly prevalent all over the world. Mycoplasma suis is the most virulent species, causing acute infectious anaemia in pigs (IAP), whereas M. parvum usually results in chronic and subclinical infections associated with performance losses. Little is known about the clinical significance of the recently discovered third porcine species 'Ca. M. haemosuis'. So far, the described pathogenic mechanisms mainly include direct destruction of erythrocytes via adhesion, invasion, eryptosis and nutrient scavenging, indirect erythrocyte lysis due to immune-mediated events and immune dysregulation processes. A review of published diagnostic data confirms PCR assays as the current standard method, with various cross-species and species-specific protocols. Overall, there is a need for further examination to obtain valuable insights for practical application, specifically regarding the importance of subclinical infections in naturally infected animals. An essential requirement for this will be to gain a more comprehensive understanding of the mechanisms operating between the host and the pathogen.
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Affiliation(s)
- Julia Ade
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany
| | - Matthias Eddicks
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany
| | - Mathias Ritzmann
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany
| | - Katharina Hoelzle
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany
| | - Ludwig E. Hoelzle
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany
| | - Julia Stadler
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany
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Oren A. On validly published names, correct names, and changes in the nomenclature of phyla and genera of prokaryotes: a guide for the perplexed. NPJ Biofilms Microbiomes 2024; 10:20. [PMID: 38467688 PMCID: PMC10928132 DOI: 10.1038/s41522-024-00494-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Bokma J, Kaske M, Vermijlen J, Stuyvaert S, Pardon B. Diagnostic performance of Mycoplasmopsis bovis antibody ELISA tests on bulk tank milk from dairy herds. BMC Vet Res 2024; 20:81. [PMID: 38443962 PMCID: PMC10916218 DOI: 10.1186/s12917-024-03927-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Testing of bulk tank milk (BTM) for Mycoplasmopsis bovis (previously Mycoplasma bovis) antibodies is increasingly popular. However the performance of some commercially available tests is unknown, and cutoff values possibly need to be adjusted in light of the purpose. Therefore, the aim of this study was to compare the diagnostic performance of three commercially available M. bovis antibody ELISAs on BTM, and to explore optimal cutoff values for screening purposes. A prospective diagnostic test accuracy study was performed on 156 BTM samples from Belgian and Swiss dairy farms using Bayesian Latent Class Analysis. Samples were initially classified using manufacturer cutoff values, followed by generated values. RESULTS Following the manufacturer's guidelines, sensitivity of 91.4%, 25.6%, 69.2%, and specificity of 67.2%, 96.8%, 85.8% were observed for ID-screen, Bio K432, and Bio K302, respectively. Optimization of cutoffs resulted in a sensitivity of 89.0%, 82.0%, and 85.5%, and a specificity of 83.4%, 75.1%, 77.2%, respectively. CONCLUSIONS The ID-screen showed the highest diagnostic performance after optimization of cutoff values, and could be useful for screening. Both Bio-X tests may be of value for diagnostic or confirmation purposes due to their high specificity.
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Affiliation(s)
- Jade Bokma
- Department of Internal Medicine, Reproduction, and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
| | - Martin Kaske
- Swiss Bovine Health Service, Zurich, Switzerland
| | | | - Sabrina Stuyvaert
- Department of Internal Medicine, Reproduction, and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Bart Pardon
- Department of Internal Medicine, Reproduction, and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Kawato S, Nozaki R, Kondo H, Hirono I. Integrase-associated niche differentiation of endogenous large DNA viruses in crustaceans. Microbiol Spectr 2024; 12:e0055923. [PMID: 38063384 PMCID: PMC10871703 DOI: 10.1128/spectrum.00559-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Crustacean genomes harbor sequences originating from a family of large DNA viruses called nimaviruses, but it is unclear why they are present. We show that endogenous nimaviruses selectively insert into repetitive sequences within the host genome, and this insertion specificity was correlated with different types of integrases, which are DNA recombination enzymes encoded by the nimaviruses themselves. This suggests that endogenous nimaviruses have colonized various genomic niches through the acquisition of integrases with different insertion specificities. Our results point to a novel survival strategy of endogenous large DNA viruses colonizing the host genomes. These findings may clarify the evolution and spread of nimaviruses in crustaceans and lead to measures to control and prevent the spread of pathogenic nimaviruses in aquaculture settings.
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Affiliation(s)
- Satoshi Kawato
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Reiko Nozaki
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
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Skrodenytė-Arbačiauskienė V, Butrimienė R, Kalnaitytė-Vengelienė A, Bagdonas S, Montvydienė D, Stankevičiūtė M, Sauliutė G, Jokšas K, Kazlauskienė N, Karitonas R, Matviienko N, Jurgelėnė Ž. A multiscale study of the effects of a diet containing CdSe/ZnS-COOH quantum dots on Salmo trutta fario L.: Potential feed-related nanotoxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167696. [PMID: 37827305 DOI: 10.1016/j.scitotenv.2023.167696] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/29/2023] [Accepted: 10/07/2023] [Indexed: 10/14/2023]
Abstract
Quantum dots (QDs) receive widespread attention in industrial and biomedical fields, but the risks posed by the use of nanoparticles to aquatic organisms and the associated toxicological effects are still not well understood. In this study, effects of the 7-day dietary exposure of Salmo trutta fario L. juveniles to CdSe/ZnS-COOH QDs were evaluated at molecular, cellular, physiological and whole-organism levels. Fish feeding with QDs-contaminated feed resulted in an increased somatic index of the liver, a genotoxic effect on peripheral blood erythrocytes, altered enzyme activity and decreased MDA level. Furthermore, Cd levels in the gills and liver tissues of the exposed fish were found to be significantly higher than in those of the control fish. Alpha diversity indexes of the gut microbiota of the QDs-exposed S. trutta fario L. individuals exhibited a decreasing trend. The principal coordinate analysis (PCoA) showed that the gut microbiota of the control fish was significantly different from that of the fish exposed to QDs (p < 0.05). Additionally, the linear discriminant analysis (LDA) performed using an effect size (LEfSe) algorithm unveiled 19 significant taxonomic differences at different taxonomic levels between the control group and the QDs-exposed group. In the QDs-exposed group, the relative abundance of the genus Citrobacter (Proteobacteria phylum) in the gut microbiota was found to be significantly increased whereas that of the genus Mycoplasma (Tenericutes phylum) significantly decreased compared to the control group. In summary, QDs-contaminated diet affects the gut microbiota of fish by significantly changing the relative abundance of some taxa, potentially leading to dysbiosis. This, together with morphophysiological, cytogenetic and biochemical changes, poses a risk to fish health.
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Affiliation(s)
| | - Renata Butrimienė
- Institute of Ecology, Nature Research Centre, Akademijos St. 2, Vilnius LT-08412, Lithuania
| | - Agnė Kalnaitytė-Vengelienė
- Laser Research Center, Physics Faculty, Vilnius University, Saulėtekio Av. 9, Vilnius LT-10222, Lithuania
| | - Saulius Bagdonas
- Laser Research Center, Physics Faculty, Vilnius University, Saulėtekio Av. 9, Vilnius LT-10222, Lithuania
| | - Danguolė Montvydienė
- Institute of Ecology, Nature Research Centre, Akademijos St. 2, Vilnius LT-08412, Lithuania
| | - Milda Stankevičiūtė
- Institute of Ecology, Nature Research Centre, Akademijos St. 2, Vilnius LT-08412, Lithuania
| | - Gintarė Sauliutė
- Institute of Ecology, Nature Research Centre, Akademijos St. 2, Vilnius LT-08412, Lithuania
| | - Kęstutis Jokšas
- Institute of Ecology, Nature Research Centre, Akademijos St. 2, Vilnius LT-08412, Lithuania; Vilnius University, Faculty of Chemistry and Geosciences, Naugarduko St. 24, LT-03225 Vilnius, Lithuania
| | - Nijolė Kazlauskienė
- Institute of Ecology, Nature Research Centre, Akademijos St. 2, Vilnius LT-08412, Lithuania
| | - Rolandas Karitonas
- Institute of Ecology, Nature Research Centre, Akademijos St. 2, Vilnius LT-08412, Lithuania
| | - Nataliia Matviienko
- Institute of Ecology, Nature Research Centre, Akademijos St. 2, Vilnius LT-08412, Lithuania; NAAS Institute of Fisheries, Obukhivska str. 135, Kyiv 03164, Ukraine
| | - Živilė Jurgelėnė
- Institute of Ecology, Nature Research Centre, Akademijos St. 2, Vilnius LT-08412, Lithuania.
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Xiu N, Yang C, Chen X, Long J, Qu P. Rare Spiroplasma Bloodstream Infection in Patient after Surgery, China, 2022. Emerg Infect Dis 2024; 30:187-189. [PMID: 38147505 PMCID: PMC10756377 DOI: 10.3201/eid3001.230858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
We report a case of Spiroplasma bloodstream infection in a patient in China who developed pulmonary infection, acute respiratory distress syndrome, sepsis, and septic shock after emergency surgery for type A aortic dissection. One organism closely related to Spiroplasma eriocheiris was isolated from blood culture and identified by whole-genome sequencing.
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Trapella G, Cinti N, Parma L, De Marco A, Dell'Acqua AN, Turroni S, Rampelli S, Scicchitano D, Iuffrida L, Bonaldo A, Franzellitti S, Candela M, Palladino G. Microbiome variation at the clam-sediment interface may explain changes in local productivity of Chamelea gallina in the North Adriatic sea. BMC Microbiol 2023; 23:402. [PMID: 38114947 PMCID: PMC10729368 DOI: 10.1186/s12866-023-03146-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND The clam Chamelea gallina is an ecologically and economically important marine species in the Northwestern Adriatic Sea, which currently suffers from occasional, and still unexplained, widespread mortality events. In order to provide some glimpses in this direction, this study explores the connections between microbiome variations at the clam-sediment interface and the nutritional status of clams collected at four Italian production sites along the Emilia Romagna coast, with different mortality incidence, higher in the Northern sites and lower in the Southern sites. RESULTS According to our findings, each production site showed a peculiar microbiome arrangement at the clam-sediment interface, with features that clearly differentiate the Northern and Southern sites, with the latter also being associated with a better nutritional status of the animal. Interestingly, the C. gallina digestive gland microbiome from the Southern sites was enriched in some health-promoting microbiome components, capable of supplying the host with essential nutrients and defensive molecules. Furthermore, in experiments conducted under controlled conditions in aquaria, we provided preliminary evidence of the prebiotic action of sediments from the Southern sites, allowing to boost the acquisition of previously identified health-promoting components of the digestive gland microbiome by clams from the Northern sites. CONCLUSIONS Taken together, our findings may help define innovative microbiome-based management strategies for the preservation of the productivity of C. gallina clams in the Adriatic Sea, through the identification and maintenance of a probiotic niche at the animal-sediment interface.
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Affiliation(s)
- Giulia Trapella
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Bologna, 40126, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
| | - Nicolò Cinti
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Bologna, 40126, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
| | - Luca Parma
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia (Bologna), 40064, Italy
| | - Antonina De Marco
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia (Bologna), 40064, Italy
| | - Andrea Nicolò Dell'Acqua
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Bologna, 40126, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Bologna, 40126, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Bologna, 40126, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
| | - Daniel Scicchitano
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Bologna, 40126, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
| | - Letizia Iuffrida
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
- Animal and Environmental Physiology Laboratory, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Ravenna, 48123, Italy
| | - Alessio Bonaldo
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia (Bologna), 40064, Italy
| | - Silvia Franzellitti
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
- Animal and Environmental Physiology Laboratory, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Ravenna, 48123, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Bologna, 40126, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
| | - Giorgia Palladino
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Bologna, 40126, Italy.
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy.
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11
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Gupta RS. Update on the genus Robertmurraya: a bacterial genus honoring Dr. Robert G.E. Murray (with some personal reminiscences). Can J Microbiol 2023; 69:387-392. [PMID: 37555510 DOI: 10.1139/cjm-2023-0070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
The genus Robertmurraya was created by my group in 2020 to recognize the contributions of Dr. Robert G.E. Murray to the field of prokaryotic taxonomy. This manuscript updates the information regarding this genus. In addition to the seven Robertmurraya species with validly published names, the work presented here shows that two species with effectively published names, "Bacillus yapensis" and "Bacillus dakarensis", and an uncharacterized Bacillus sp. Y1 are also affiliated with this genus. Based on these results, reclassification of "Bacillus yapensis" as a novel species Robertmurraya yapensis sp. nov. is proposed. It is also suggested that "Bacillus dakarensis", for which strains are not available from culture collections, should also be recognized as "Robertmurraya dakarensis". This article also reflects on the serendipitous way I came to know Dr. Murray and his extensive interactions with me and strong support for our work for more than 10 years. Dr. Murray also introduced me and our work to his friend and contemporary Dr. Peter Sneath, who like him also contributed extensively to the field of prokaryotic taxonomy. This introduction led to a fruitful collaboration with Dr. Sneath leading to a joint publication describing the use of the Character Compatibility approach to molecular sequence data.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada L8N 3Z5
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12
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Bailey NP, Shao Y, Du S, Foster PG, Fettweis J, Hall N, Wang Z, Hirt RP. Evolutionary conservation of Trichomonas-mycoplasma symbiosis across the host species barrier. Front Microbiol 2023; 14:1242275. [PMID: 37808290 PMCID: PMC10557491 DOI: 10.3389/fmicb.2023.1242275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction The protozoan parasite Trichomonas vaginalis is the most common cellular sexually transmitted disease in humans, and the closely related species Trichomonas gallinae is an avian parasite of ecological and economic importance. Phylogenetic evidence suggests T. vaginalis arose during bird to human transmission of a T. gallinae-like ancestor. Trichomonas vaginalis shares a strong clinical association with the independent sexually transmitted pathogen Metamycoplasma (formerly Mycoplasma) hominis, and the uncultured bacterium "Candidatus Malacoplasma (formerly Mycoplasma) girerdii," with the latter association being an order of magnitude stronger. Both bacterial species have been shown to profoundly influence T. vaginalis growth, energy production and virulence-associated mechanisms. Methods Evidence for a novel Malacoplasma sp. was discovered by in vivo Illumina metatranscriptomics sequencing of the T. gallinae-infected pigeon mouth. We leveraged published 16S rDNA profiling data from digestive tract of 12 healthy and 24 T. gallinae-infected pigeons to investigate association between the novel Malacoplasma sp. and T. gallinae. We utilised Illumina metagenomics sequencing targeted to pigeon oral and crop samples infected with the novel Malacoplasma sp. to generate its full-length genome sequence. Sequence similarity network analysis was used to compare annotated proteins from the novel Malacoplasma sp. with a range of other related species. Results Here we present evidence for a novel Malacoplasma species, related to "Ca. M. girerdii," that is strongly associated with T. gallinae in the upper digestive tract of domestic pigeons. Analysis of the genome sequence revealed gene features apparently specific to a Trichomonas-symbiotic Malacoplasma lineage. Discussion These data support a model of long-term association between Trichomonas and Malacoplasma spp. that has been conserved across diversification of the Trichomonas lineage and the host species barrier from birds to human.
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Affiliation(s)
- Nicholas P. Bailey
- Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Yuxin Shao
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shaodua Du
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | | | | | - Neil Hall
- Earlham Institute, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, United Kingdom
| | - Zheng Wang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Robert P. Hirt
- Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
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13
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Margarita V, Congiargiu A, Diaz N, Fiori PL, Rappelli P. Mycoplasma hominis and Candidatus Mycoplasma girerdii in Trichomonas vaginalis: Peaceful Cohabitants or Contentious Roommates? Pathogens 2023; 12:1083. [PMID: 37764891 PMCID: PMC10535475 DOI: 10.3390/pathogens12091083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/20/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Trichomonas vaginalis is a pathogenic protozoan diffused worldwide capable of infecting the urogenital tract in humans, causing trichomoniasis. One of its most intriguing aspects is the ability to establish a close relationship with endosymbiotic microorganisms: the unique association of T. vaginalis with the bacterium Mycoplasma hominis represents, to date, the only example of an endosymbiosis involving two true human pathogens. Since its discovery, several aspects of the symbiosis between T. vaginalis and M. hominis have been characterized, demonstrating that the presence of the intracellular guest strongly influences the pathogenic characteristics of the protozoon, making it more aggressive towards host cells and capable of stimulating a stronger proinflammatory response. The recent description of a further symbiont of the protozoon, the newly discovered non-cultivable mycoplasma Candidatus Mycoplasma girerdii, makes the picture even more complex. This review provides an overview of the main aspects of this complex microbial consortium, with particular emphasis on its effect on protozoan pathobiology and on the interplays among the symbionts.
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Affiliation(s)
- Valentina Margarita
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy; (V.M.); (A.C.); (N.D.); (P.L.F.)
- Mediterranean Centre for Disease Control (MCDC), 07110 Sassari, Italy
| | - Antonella Congiargiu
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy; (V.M.); (A.C.); (N.D.); (P.L.F.)
| | - Nicia Diaz
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy; (V.M.); (A.C.); (N.D.); (P.L.F.)
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy; (V.M.); (A.C.); (N.D.); (P.L.F.)
- Mediterranean Centre for Disease Control (MCDC), 07110 Sassari, Italy
- Microbiology Unit, University Hospital of Sassari (AOU), 07110 Sassari, Italy
| | - Paola Rappelli
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy; (V.M.); (A.C.); (N.D.); (P.L.F.)
- Mediterranean Centre for Disease Control (MCDC), 07110 Sassari, Italy
- Microbiology Unit, University Hospital of Sassari (AOU), 07110 Sassari, Italy
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14
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Gupta RS, Kanter-Eivin DA. AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species. Int J Syst Evol Microbiol 2023; 73. [PMID: 37159410 DOI: 10.1099/ijsem.0.005844] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Taxon-specific conserved signature indels (CSIs) in genes/proteins provide reliable molecular markers (synapomorphies) for unambiguous demarcation of taxa of different ranks in molecular terms and for genetic, biochemical and diagnostic studies. Because of their predictive abilities, the shared presence of known taxon-specific CSIs in genome sequences has proven useful for taxonomic purposes. However, the lack of a convenient method for identifying the presence of known CSIs in genome sequences has limited their utility for taxonomic and other studies. We describe here a web-based tool/server (AppIndels.com) that identifies the presence of known and validated CSIs in genome sequences and uses this information for predicting taxonomic affiliation. The utility of this server was tested by using a database of 585 validated CSIs, which included 350 CSIs specific for ≈45 Bacillales genera, with the remaining CSIs being specific for members of the orders Neisseriales, Legionellales and Chlorobiales, family Borreliaceae, and some Pseudomonadaceae species/genera. Using this server, genome sequences were analysed for 721 Bacillus strains of unknown taxonomic affiliation. Results obtained showed that 651 of these genomes contained significant numbers of CSIs specific for the following Bacillales genera/families: Alkalicoccus, 'Alkalihalobacillaceae', Alteribacter, Bacillus Cereus clade, Bacillus Subtilis clade, Caldalkalibacillus, Caldibacillus, Cytobacillus, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Mesobacillus, Metabacillus, Neobacillus, Niallia, Peribacillus, Priestia, Pseudalkalibacillus, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sporosarcina, Sutcliffiella, Weizmannia and Caryophanaceae. Validity of the taxon assignment made by the server was examined by reconstructing phylogenomic trees. In these trees, all Bacillus strains for which taxonomic predictions were made correctly branched with the indicated taxa. The unassigned strains likely correspond to taxa for which CSIs are lacking in our database. Results presented here show that the AppIndels server provides a useful new tool for predicting taxonomic affiliation based on shared presence of the taxon-specific CSIs. Some caveats in using this server are discussed.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario CA L8N 3Z5, Canada
| | - David A Kanter-Eivin
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario CA L8N 3Z5, Canada
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15
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Huyben D, Jarau M, MacInnes J, Stevenson R, Lumsden J. Impact of Infection with Flavobacterium psychrophilum and Antimicrobial Treatment on the Intestinal Microbiota of Rainbow Trout. Pathogens 2023; 12:pathogens12030454. [PMID: 36986376 PMCID: PMC10055933 DOI: 10.3390/pathogens12030454] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/01/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023] Open
Abstract
The diversity and composition of intestinal microbiota in rainbow trout have been studied using next-generation sequencing (NGS), although few studies have examined the effects of antimicrobials. We evaluated the effect of antibiotics florfenicol and erythromycin and infection with or without Flavobacterium psychrophilum on the intestinal microbiota in rainbow trout juveniles (30–40 g) using NGS. Prophylactic oral antibiotic treatments were administered for 10 days before groups of fish were injected intraperitoneally with virulent F. psychrophilum. Intestinal content (allochthonous bacteria) was collected at day −11, 0, 12, and 24 p.i., and the v3–v4 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Before prophylactic treatment, Tenericutes and Proteobacteria were the most abundant phyla identified and Mycoplasma was the most abundant genus. Fish infected with F. psychrophilum had decreased alpha diversity and a high abundance of Mycoplasma. Fish administered florfenicol had increased alpha diversity compared to the control at day 24 p.i., although both florfenicol and erythromycin-treated fish had a higher abundance of potential pathogens, specifically Aeromonas, Pseudomonas, and Acinetobacter. Mycoplasma disappeared after treatment but appeared again after day 24. This study demonstrates that prophylactic oral treatment with antibiotics florfenicol and erythromycin as well as F. psychrophilum infection changed the composition of intestinal microbiota in rainbow trout juveniles that did not recover by day 24 p.i. and further long-term effects on the host need to be investigated.
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Affiliation(s)
- David Huyben
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Maureen Jarau
- Department of Pathobiology, University of Guelph, ON N1G 2W1, Canada
| | - Janet MacInnes
- Department of Pathobiology, University of Guelph, ON N1G 2W1, Canada
| | - Roselynn Stevenson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - John Lumsden
- Department of Pathobiology, University of Guelph, ON N1G 2W1, Canada
- Correspondence:
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16
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Munson E, Lawhon SD, Burbick CR, Zapp A, Villaflor M, Thelen E. An Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Domestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0028122. [PMID: 36533907 PMCID: PMC9945509 DOI: 10.1128/jcm.00281-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations. Expansion of research on the microbiota of humans, animals, and insects has significant potential impacts on the taxonomy of organisms of clinical interest. Implications of taxonomic changes may be especially important when considering zoonotic diseases. Here, we address novel taxonomy and nomenclature revisions of veterinary significance. Noteworthy discussion centers around descriptions of novel mastitis pathogens in Streptococcaceae, Staphylococcaceae, and Actinomycetaceae; bovine reproductive tract pathogens in Corynebacteriaceae; novel members of Mannheimia spp., Leptospira spp., and Mycobacterium spp.; the transfer of Ochrobactrum spp. to Brucella spp.; and revisions to the genus Mycoplasma.
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Affiliation(s)
- Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Sara D. Lawhon
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Claire R. Burbick
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Amanda Zapp
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Maia Villaflor
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Elizabeth Thelen
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
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17
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Lawhon SD, Burbick CR, Munson E, Zapp A, Thelen E, Villaflor M. Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0142522. [PMID: 36533958 PMCID: PMC9945507 DOI: 10.1128/jcm.01425-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.
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Affiliation(s)
- Sara D. Lawhon
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Claire R. Burbick
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Amanda Zapp
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Elizabeth Thelen
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Maia Villaflor
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
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18
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Galosi L, Ridolfi N, Fellini C, Pelizzone I, Cusaro S, Marchetti G, Canonico M, Ghelfi E, Di Girolamo N, Preziuso S. Detection and Identification of Mycoplasmopsis agassizii in Captive Tortoises with Different Clinical Signs in Italy. Animals (Basel) 2023; 13:ani13040588. [PMID: 36830375 PMCID: PMC9951701 DOI: 10.3390/ani13040588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023] Open
Abstract
Mycoplasmopsis agassizii causes the Upper Respiratory Tract Disease (URTD) in tortoises. The severity of the disease usually ranges from mild to severe respiratory signs. Animals can recover, die, or become asymptomatic carriers and are source of infection for other tortoises. This study describes (i) the clinical history and the results obtained in ten years of diagnostic PCR activity for detecting M. agassizii in different species of captive tortoises in Italy, and (ii) the phylogenetic analysis of the 16S rRNA gene sequences of M. agassizii. A total of 26.0% out of 169 samples resulted positive by PCR and 32 out of 75 (42.7%) animals with symptoms were positive. Sequences ob-tained from the PCR products were conserved, differed from the sequence of the M. agassizii type strain PS6, and were identical to many M. agassizii sequences deposited in databases. In particular, the sequences were identical or very similar to sequences obtained previously from tortoises in It-aly. Since samples collected from different anatomical sites resulted positive, it is suggested that pools of conjunctival, nasal and oral swabs are tested for diagnostic purpose in both symptomatic and asymptomatic animals.
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Affiliation(s)
- Livio Galosi
- School of Biosciences and Veterinary Medicine, University of Camerino, 62024 Matelica, Italy
| | | | | | - Igor Pelizzone
- Ambulatorio Veterinario Belvedere, 42123 Reggio Emilia, Italy
| | - Stefano Cusaro
- Ambulatorio Veterinario Associato XXIII Marzo, 28100 Novara, Italy
| | | | - Matteo Canonico
- Nuovo Ambulatorio Veterinario Artemis, 60019 Senigallia, Italy
| | - Elena Ghelfi
- Ambulatorio Veterinario Associato Ghelfi Nieddu, 27100 Pavia, Italy
| | - Nicola Di Girolamo
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Silvia Preziuso
- School of Biosciences and Veterinary Medicine, University of Camerino, 62024 Matelica, Italy
- Correspondence:
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19
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Judicial Opinions 112–122. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Opinion 112 denies the request to place
Seliberia
Aristovskaya and Parinkina 1963 (Approved Lists 1980) on the list of rejected names because the information provided is insufficient. For the same reason, Opinion 113 denies the request to reject
Shewanella irciniae
Lee et al. 2006 and Opinion 114 denies the request to reject the name
Enterobacter siamensis
Khunthongpan et al. 2014. Opinion 115 rejects the epithet of
Moorella thermoautotrophica
(Wiegel et al. 1981) Collins et al. 1994, which is regarded as a nomen confusum. To assess the consequences of Rule 8, Opinion 116 revisits names of taxa above the rank of genus which should comprise the stem of the name of a nomenclatural type and a category-specific ending but fail to do so. Such names should be orthographically corrected if the sole error is the inadvertent usage of an incorrect stem or be regarded as illegitimate if otherwise. The necessary corrections are made for a number of names. In Opinion 117, the request to designate
Methylothermus subterraneus
Hirayama et al. 2011 as the type species of the genus
Methylothermus
is denied because an equivalent action compatible with the Code was already conducted. In Opinion 118, the possible orthographical correction of the name
Flaviaesturariibacter
is treated, as are the analogous cases of
Fredinandcohnia
and
Hydrogeniiclostidium
. The genus names are corrected to Flaviaestuariibacter, Ferdinandcohnia and
Hydrogeniiclostridium
, respectively. Opinion 119 concludes that assigning
Actinomycetales
Buchanan 1917 (Approved Lists 1980) as nomenclatural type of the class
Actinobacteria
Stackebrandt et al. 1997 would not render that name legitimate if Rule 8 remained retroactive. The request is granted but
Actinomycetales
is also assigned as type of
Actinomycetes
Krassilnikov 1949 (Approved Lists 1980). In Opinion 120, the possible orthographical correction of the name
Amycolatopsis albidoflavus
is treated. It is grammatically corrected to Amycolatopsis albidoflava. Six names which could according to Rule 61 be grammatically corrected by anyone are also corrected. Opinion 121 denies the request to revise Opinion 69 and notes that Opinion 69 does not have the undesirable consequences emphasized in the request. In Opinion 122, the request to reject various taxon names of
Mollicutes
proposed in 2018 is denied because it is based on misinterpretations of the Code, which are clarified. Alternative ways to solve the perceived problems are outlined. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.
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McKee RK, Buhlmann KA, Moore CT, Allender MC, Stacy NI, Tuberville TD. Island of misfit tortoises: waif gopher tortoise health assessment following translocation. CONSERVATION PHYSIOLOGY 2022; 10:coac051. [PMID: 37501911 PMCID: PMC9328764 DOI: 10.1093/conphys/coac051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/23/2022] [Accepted: 07/05/2022] [Indexed: 07/29/2023]
Abstract
Translocation, the intentional movement of animals from one location to another, is a common management practice for the gopher tortoise (Gopherus polyphemus). Although the inadvertent spread of pathogens is a concern with any translocation effort, waif tortoises-individuals that have been collected illegally, injured and rehabilitated or have unknown origins-are generally excluded from translocation efforts due to heightened concerns of introducing pathogens and subsequent disease to naïve populations. However, repurposing these long-lived animals for species recovery is desirable when feasible, and introducing waif tortoises may bolster small populations facing extirpation. The objective of this study was to assess the health of waif tortoises experimentally released at an isolated preserve in Aiken County, SC, USA. Our assessments included visual examination, screening for 14 pathogens using conventional or quantitative polymerase chain reaction (qPCR) and haematological evaluation. Of the 143 individuals assessed in 2017 and 2018, most individuals (76%; n = 109 of 143) had no overt clinical evidence of disease and, when observed, clinical findings were mild. In both years, we detected two known tortoise pathogens, Mycoplasma agassizii and Mycoplasma testudineum, at a prevalence of 10.2-13.9% and 0.0-0.8%, respectively. Additionally, we found emydid Mycoplasma, a bacterium commonly found in box turtles (Terrapene spp.), in a single tortoise that showed no clinical evidence of infection. The presence of nasal discharge was an important, but imperfect, predictor of Mycoplasma spp. infection in translocated tortoises. Hemogram data were comparable with wild populations. Our study is the first comprehensive effort to assess pathogen prevalence and hemogram data of waif gopher tortoises following translocation. Although caution is warranted and pathogen screening necessary, waif tortoises may be an important resource for establishing or augmenting isolated populations when potential health risks can be managed.
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Affiliation(s)
- Rebecca K McKee
- Corresponding author: Department of Wildlife Ecology and Conservation, University of Florida, Mailing: P.O. Box 110430, 110 Newins-Ziegler Hall, Gainesville, FL 32611, USA. Tel: 828-226-0926.
| | - Kurt A Buhlmann
- Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, SC 29802, USA
| | - Clinton T Moore
- U.S. Geological Survey, Georgia Cooperative Fish and Wildlife Research Unit, 180 E Green Street, Athens, GA, 30602, USA
| | - Matthew C Allender
- Wildlife Epidemiology Lab, College of Veterinary Medicine, University of Illinois, 2001 S. Lincoln Ave., Urbana, IL 61802, USA
| | - Nicole I Stacy
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave, Gainesville, FL 32610, USA
| | - Tracey D Tuberville
- Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, SC 29802, USA
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21
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Margarita V, Bailey NP, Rappelli P, Diaz N, Dessì D, Fettweis JM, Hirt RP, Fiori PL. Two Different Species of Mycoplasma Endosymbionts Can Influence Trichomonas vaginalis Pathophysiology. mBio 2022; 13:e0091822. [PMID: 35608298 PMCID: PMC9239101 DOI: 10.1128/mbio.00918-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/28/2022] [Indexed: 12/12/2022] Open
Abstract
Trichomonas vaginalis can host the endosymbiont Mycoplasma hominis, an opportunistic pathogenic bacterium capable of modulating T. vaginalis pathobiology. Recently, a new noncultivable mycoplasma, "Candidatus Mycoplasma girerdii," has been shown to be closely associated with women affected by trichomoniasis, suggesting a biological association. Although several features of "Ca. M. girerdii" have been investigated through genomic analysis, the nature of the potential T. vaginalis-"Ca. M. girerdii" consortium and its impact on the biology and pathogenesis of both microorganisms have not yet been explored. Here, we investigate the association between "Ca. M. girerdii" and T. vaginalis isolated from patients affected by trichomoniasis, demonstrating their intracellular localization. By using an in vitro model system based on single- and double-Mycoplasma infection of Mycoplasma-free isogenic T. vaginalis, we investigated the ability of the protist to establish a relationship with the bacteria and impact T. vaginalis growth. Our data indicate likely competition between M. hominis and "Ca. M. girerdii" while infecting trichomonad cells. Comparative dual-transcriptomics data showed major shifts in parasite gene expression in response to the presence of Mycoplasma, including genes associated with energy metabolism and pathogenesis. Consistent with the transcriptomics data, both parasite-mediated hemolysis and binding to host epithelial cells were significantly upregulated in the presence of either Mycoplasma species. Taken together, these results support a model in which this microbial association could modulate the virulence of T. vaginalis. IMPORTANCE T. vaginalis and M. hominis form a unique case of endosymbiosis that modulates the parasite's pathobiology. Recently, a new nonculturable mycoplasma species ("Candidatus Mycoplasma girerdii") has been described as closely associated with the protozoon. Here, we report the characterization of this endosymbiotic relationship. Clinical isolates of the parasite demonstrate that mycoplasmas are common among trichomoniasis patients. The relationships are studied by devising an in vitro system of single and/or double infections in isogenic protozoan recipients. Comparative growth experiments and transcriptomics data demonstrate that the composition of different microbial consortia influences the growth of the parasite and significantly modulates its transcriptomic profile, including metabolic enzymes and virulence genes such as adhesins and pore-forming proteins. The data on modulation from RNA sequencing (RNA-Seq) correlated closely with those of the cytopathic effect and adhesion to human target cells. We propose the hypothesis that the presence and the quantitative ratios of endosymbionts may contribute to modulating protozoan virulence. Our data highlight the importance of considering pathogenic entities as microbial ecosystems, reinforcing the importance of the development of integrated diagnostic and therapeutic strategies.
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Affiliation(s)
| | - Nicholas P. Bailey
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Paola Rappelli
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Mediterranean Center for Disease Control (MCDC), Sassari, Italy
| | - Nicia Diaz
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Daniele Dessì
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Mediterranean Center for Disease Control (MCDC), Sassari, Italy
| | - Jennifer M. Fettweis
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Obstetrics and Gynecology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Robert P. Hirt
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Mediterranean Center for Disease Control (MCDC), Sassari, Italy
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22
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Dawood A, Algharib SA, Zhao G, Zhu T, Qi M, Delai K, Hao Z, Marawan MA, Shirani I, Guo A. Mycoplasmas as Host Pantropic and Specific Pathogens: Clinical Implications, Gene Transfer, Virulence Factors, and Future Perspectives. Front Cell Infect Microbiol 2022; 12:855731. [PMID: 35646746 PMCID: PMC9137434 DOI: 10.3389/fcimb.2022.855731] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/04/2022] [Indexed: 12/28/2022] Open
Abstract
Mycoplasmas as economically important and pantropic pathogens can cause similar clinical diseases in different hosts by eluding host defense and establishing their niches despite their limited metabolic capacities. Besides, enormous undiscovered virulence has a fundamental role in the pathogenesis of pathogenic mycoplasmas. On the other hand, they are host-specific pathogens with some highly pathogenic members that can colonize a vast number of habitats. Reshuffling mycoplasmas genetic information and evolving rapidly is a way to avoid their host's immune system. However, currently, only a few control measures exist against some mycoplasmosis which are far from satisfaction. This review aimed to provide an updated insight into the state of mycoplasmas as pathogens by summarizing and analyzing the comprehensive progress, current challenge, and future perspectives of mycoplasmas. It covers clinical implications of mycoplasmas in humans and domestic and wild animals, virulence-related factors, the process of gene transfer and its crucial prospects, the current application and future perspectives of nanotechnology for diagnosing and curing mycoplasmosis, Mycoplasma vaccination, and protective immunity. Several questions remain unanswered and are recommended to pay close attention to. The findings would be helpful to develop new strategies for basic and applied research on mycoplasmas and facilitate the control of mycoplasmosis for humans and various species of animals.
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Affiliation(s)
- Ali Dawood
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
- Hubei Hongshan Laboratory, Wuhan, China
| | - Samah Attia Algharib
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, HZAU, Wuhan, China
- Department of Clinical Pathology, Faculty of Veterinary Medicine, Benha University, Toukh, Egypt
| | - Gang Zhao
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| | - Tingting Zhu
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| | - Mingpu Qi
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| | - Kong Delai
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhiyu Hao
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| | - Marawan A. Marawan
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- Infectious Diseases, Faculty of Veterinary Medicine, Benha University, Toukh, Egypt
| | - Ihsanullah Shirani
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- Para-Clinic Department, Faculty of Veterinary Medicine, Jalalabad, Afghanistan
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
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23
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Winter JM, Wellehan JFX, Apakupakul K, Palmer J, Brenn-White M, Standorf K, Berry KH, Childress AL, Koplos P, Garner MM, Deem SL. A novel herpesvirus detected in 3 species of chelonians. J Vet Diagn Invest 2022; 34:594-601. [PMID: 35459421 PMCID: PMC9266504 DOI: 10.1177/10406387221092048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Herpesviruses are found in free-living and captive chelonian populations, often in association with morbidity and mortality. To date, all known chelonian herpesviruses fall within the subfamily Alphaherpesvirinae. We detected a novel herpesvirus in 3 species of chelonians: a captive leopard tortoise (Stigmochelys pardalis) in western TX, USA; a steppe tortoise (Testudo [Agrionemys] horsfieldii) found near Fort Irwin, CA, USA; and 2 free-living, three-toed box turtles (Terrapene mexicana triunguis) found in Forest Park, St. Louis, MO. The leopard tortoise was coinfected with the tortoise intranuclear coccidian and had clinical signs of upper respiratory tract disease. The steppe tortoise had mucopurulent nasal discharge and lethargy. One of the three-toed box turtles had no clinical signs; the other was found dead with signs of trauma after being observed with blepharedema, tympanic membrane swelling, cervical edema, and other clinical signs several weeks prior to death. Generally, the branching order of the turtle herpesviruses mirrors the divergence patterns of their hosts, consistent with codivergence. Based on phylogenetic analysis, this novel herpesvirus clusters with a clade of viruses that infect emydid hosts and is likely of box turtle origin. Therefore, we suggest the name terrapene alphaherpesvirus 3 (TerAHV3) for the novel virus. This virus also has the ability to host-jump to tortoises, and previously documented herpesviral morbidity tends to be more common in aberrant hosts. The relationship between clinical signs and infection with TerAHV3 in these animals is unclear, and further investigation is merited.
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Affiliation(s)
- John M Winter
- College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - James F X Wellehan
- Zoological Medicine Service, Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | | | - Jamie Palmer
- Institute for Conservation Medicine, Saint Louis Zoo, St. Louis, MO, USA
| | - Maris Brenn-White
- Institute for Conservation Medicine, Saint Louis Zoo, St. Louis, MO, USA
| | | | - Kristin H Berry
- Western Ecological Research Center, United States Geological Survey, Reno, NV, USA
| | - April L Childress
- Zoological Medicine Service, Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Peter Koplos
- El Paso Veterinary Specialty Center, El Paso, TX, USA
| | | | - Sharon L Deem
- Institute for Conservation Medicine, Saint Louis Zoo, St. Louis, MO, USA
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24
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Chen R, Zhao L, Gan R, Feng Z, Cui C, Xie X, Hao F, Zhang Z, Wang L, Ran T, Wang W, Zhang S, Li Y, Zhang W, Pang M, Xiong Q, Shao G. Evidence for the Rapid and Divergent Evolution of Mycoplasmas: Structural and Phylogenetic Analysis of Enolases. Front Mol Biosci 2022; 8:811106. [PMID: 35145997 PMCID: PMC8822174 DOI: 10.3389/fmolb.2021.811106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 12/29/2021] [Indexed: 12/21/2022] Open
Abstract
Mycoplasmas are a group of prokaryotes without cell walls that have evolved through several rounds of degenerative evolution. With a low cell DNA G + C content and definitively long genetic lineages, mycoplasmas are thought to be in a state of rapid evolution. However, little associated evidence has been provided. Enolase is a key enzyme in glycolysis that is widely found in all species from the three domains, and it is evolutionarily conserved. In our previous studies, enolase acted as a virulence factor and participated in cell-surface adhesion in Mycoplasma hyopneumoniae. Furthermore, unique loop regions were first found in the crystal structure of Mhp Eno. Here, enolase structures from Mycoplasma pneumoniae and Mycoplasma bovis were determined. An extra helix 7 is specific and conservatively found in almost all mycoplasma enolases, as confirmed by crystal structures and sequence alignment. Particular motifs for helix 7, which is composed of F-K/G-K-L/F-K-X-A-I, have been proposed and could be regarded as molecular markers. To our surprise, the genetic distances between any two mycoplasma enolases were obviously longer than those between the two corresponding species themselves, indicating divergent evolution of mycoplasma enolases, whereas no horizontal gene transfer was detected in mycoplasma enolase genens. Furthermore, different evolutionary patterns were adopted by different loop regions of mycoplasma enolase. Enolases from different Mycoplasma species also showed different affinities for PLG and fibronectin. Our results indicate the rapid and divergent evolution of mycoplasma enolase and mycoplasmas. This study will also aid understanding the independent evolution of Mycoplasma species after separation from their common ancestor.
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Affiliation(s)
- Rong Chen
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Lin Zhao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Rong Gan
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zhixin Feng
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Chenxi Cui
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xing Xie
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Fei Hao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhenzhen Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Li Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Tingting Ran
- Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Weiwu Wang
- Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Shuijun Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yufeng Li
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wei Zhang
- Key Lab of Animal Bacteriology of Ministry of Agriculture, OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Wei Zhang, ; Maoda Pang, ; Qiyan Xiong,
| | - Maoda Pang
- State Key Laboratory Cultivation Base of MOST, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- *Correspondence: Wei Zhang, ; Maoda Pang, ; Qiyan Xiong,
| | - Qiyan Xiong
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- *Correspondence: Wei Zhang, ; Maoda Pang, ; Qiyan Xiong,
| | - Guoqing Shao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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25
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Gupta RS. Microbial Taxonomy: How and Why Name Changes Occur and Their Significance for (Clinical) Microbiology. Clin Chem 2021; 68:134-137. [PMID: 34969111 DOI: 10.1093/clinchem/hvab188] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/03/2021] [Indexed: 11/12/2022]
Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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26
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Smolec D, Ekiel A, Kłuciński P, Kawecki J. Occurrence of urogenital mycoplasmas in men with the common genitourinary diseases. Braz J Microbiol 2021; 52:2013-2019. [PMID: 34561845 PMCID: PMC8578499 DOI: 10.1007/s42770-021-00620-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/19/2021] [Indexed: 10/31/2022] Open
Abstract
Many serious and fatal infections with urogenital mycoplasmas in immunocompromised patients have been reported. M. genitalium is recognized as a cause of male urethritis and other common genitourinary diseases. The aim of the study was to estimate prevalence of urogenital mycoplasmas which can cause complications in men with common genitourinary diseases. Study included 85 men with genitourinary tract carcinoma (n = 35), urolithiasis (n = 36), and BPH (benign prostatic hyperplasia) (n = 14). The control group consisted of 50 healthy men. FVU (first void urine) samples were examined by PCR for the presence of urogenital mycoplasmas DNA. Occurrence of urogenital mycoplasmas was significantly more common in study group compared with control 24/85 (28.2%) and 7/50 (14%), respectively (p = 0.05). In men with urolithiasis, positive results for mycoplasmas DNA were significantly more frequent than in control: 33.3% vs. 14% (p < 0.05). In patients with urolithiasis DNA of U. urealyticum was most often found, while in the genitourinary carcinoma and BPH groups, U. parvum was more frequent. Incidence of M. fermentans was also significantly higher in the urolithiasis group vs. control (p = 0.03). A higher percentage of positive results for urogenital mycoplasma DNA in study group has been found. Further studies are required to confirm the role of urogenital mycoplasmas in the development of infectious complications among patients with urolithiasis, genitourinary carcinoma, and BPH.
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Affiliation(s)
- Dominika Smolec
- Department of Medical Microbiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Medyków 18 Street, 40-752, Katowice, Poland.
| | - Alicja Ekiel
- Department of Medical Microbiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Medyków 18 Street, 40-752, Katowice, Poland
| | - Piotr Kłuciński
- Department of Medical Microbiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Medyków 18 Street, 40-752, Katowice, Poland.,Med Holding Emil Michalowski Specialist Hospital, Katowice, Poland
| | - Jan Kawecki
- Med Holding Emil Michalowski Specialist Hospital, Katowice, Poland
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27
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Seasonal Changes in the Distinct Taxonomy and Function of the Gut Microbiota in the Wild Ground Squirrel ( Spermophilus dauricus). Animals (Basel) 2021; 11:ani11092685. [PMID: 34573650 PMCID: PMC8469230 DOI: 10.3390/ani11092685] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/28/2021] [Accepted: 09/02/2021] [Indexed: 12/26/2022] Open
Abstract
Seasonal breeding is a normal phenomenon in which animals adapt to natural selection and reproduce only in specific seasons. Large studies have reported that the gut microbiota is closely related to reproduction. The purpose of this study was to explore the distinct taxonomy and function of the gut microbiota in the breeding and non-breeding seasons of the wild ground squirrel (Spermophilus dauricus). The 16S rRNA gene sequencing technology was utilized to sequence the gut microbiota of the wild ground squirrel. PICRUSt analysis was also applied to predict the function of the gut microbiota. The results suggested that the main components of the gut microbiota in all samples were Firmicutes (61.8%), Bacteroidetes (32.4%), and Proteobacteria (3.7%). Microbial community composition analyses revealed significant differences between the breeding and non-breeding seasons. At the genus level, Alistipes, Mycoplasma, Anaerotruncus, and Odoribacter were more abundant in the non-breeding season, while Blautia and Streptococcus were more abundant in the breeding season. The results of a functional prediction suggested that the relative abundance of functional categories that were related to lipid metabolism, carbohydrate metabolism, and nucleotide metabolism increased in the breeding season. The relative abundance of energy metabolism, transcription, and signal transduction increased in the non-breeding season. Overall, this study found differences in the taxonomy and function of the gut microbiota of the wild ground squirrel between the breeding and non-breeding seasons, and laid the foundation for further studies on the relationship between the gut microbiota and seasonal breeding.
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28
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Käbisch L, Schink AK, Kehrenberg C, Schwarz S. Provisional Use of CLSI-Approved Quality Control Strains for Antimicrobial Susceptibility Testing of Mycoplasma ( 'Mesomycoplasma') hyorhinis. Microorganisms 2021; 9:microorganisms9091829. [PMID: 34576724 PMCID: PMC8466829 DOI: 10.3390/microorganisms9091829] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial susceptibility testing (AST) should be conducted in a standardized manner prior to the start of an antimicrobial treatment. For fastidious bacteria, such as porcine Mycoplasma ('Mesomycoplasma') spp., specifically M. hyorhinis, neither guidelines or standards for the performance of AST, nor quality control strains for the validation of AST results are approved by organizations like the Clinical and Laboratory Standards Institute (CLSI) or the European Committee on Antimicrobial Susceptibility Testing (EUCAST). The CLSI- and EUCAST-approved quality control strains Enterococcus faecalis ATCC 29212 and Staphylococcus aureus ATCC 29213 were chosen to validate AST by broth microdilution using modified Friis broth, developed as growth medium for porcine Mycoplasma ('Mesomycoplasma') spp. The antimicrobial agents doxycycline, enrofloxacin, erythromycin, florfenicol, gentamicin, marbofloxacin, tetracycline, tiamulin, tilmicosin, tulathromycin, and tylosin were examined using customized SensititreTM microtiter plates. Minimal inhibitory concentrations, determined after 24, 48, and 72 h, were mostly within the CLSI-approved quality control ranges for defined antimicrobial agents. We propose the use of the combination of E. faecalis ATCC 29212 and S. aureus ATCC 29213 as surrogate quality control strains for the validation of future AST results obtained for M. hyorhinis by broth microdilution using modified Friis broth.
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Affiliation(s)
- Lisa Käbisch
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany; (L.K.); (S.S.)
- Department of Veterinary Medicine, Institute for Veterinary Food Science, Justus-Liebig-University Gießen, 35392 Gießen, Germany;
| | - Anne-Kathrin Schink
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany; (L.K.); (S.S.)
- Correspondence: ; Tel.: +49-308-386-3162
| | - Corinna Kehrenberg
- Department of Veterinary Medicine, Institute for Veterinary Food Science, Justus-Liebig-University Gießen, 35392 Gießen, Germany;
| | - Stefan Schwarz
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany; (L.K.); (S.S.)
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29
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Desiderio TM, Stacy NI, Ossiboff RJ, Iredale M, Archer LL, Alexander AB, Heard DJ, Crevasse SE, Craft WF, Fredholm DVE, Donnelly KA, Rosenberg JF, Childress AL, Russell K, Wellehan JFX. Identification of a novel mortality-associated Helicobacter species in gopher tortoises (Gopherus polyphemus), qPCR test development and validation, and correlation with mortality in a wildlife rehabilitation population. Vet Microbiol 2021; 259:109136. [PMID: 34214906 DOI: 10.1016/j.vetmic.2021.109136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/25/2021] [Indexed: 11/27/2022]
Abstract
The genus Helicobacter includes spiral-shaped bacteria in the phylum Proteobacteria, class Epsilonproteobacteria, order Campylobacteriales, that have been associated with disease in animals, including reptiles. Three wild gopher tortoise (Gopherus polyphemus) index cases presented between 2012 and 2019 with nasal discharge, lethargy, and weight loss. Cytological examination of nasal discharge from all 3 tortoises identified marked heterophilic and mild histiocytic rhinitis with abundant extracellular and phagocytized spiral shaped bacteria that stained positive with Warthin-Starry stain. Polymerase chain reaction (PCR) and sequencing of the 16S rRNA gene revealed this to be a novel Helicobacter species. Two tortoises died despite treatment attempts, and the third was moribund and was euthanized. Histological examination of the nasal mucosa (n = 3) showed granulocytic to lymphocytic rhinitis with variable mucosal hyperplasia, erosion, and ulceration; Warthin-Starry staining highlighted the presence of spiral bacteria in the untreated tortoise. Genus-specific primers were designed, and the gyrA and groEL genes were amplified by PCR and sequenced. Phylogenetic analysis shows that this organism and other previously characterized Helicobacter from tortoises form a clade. Development and cross-validation of two qPCR diagnostic assays for the gyrA and groEL genes showed significant correlation of the results of two assays (P < 0.0001). These assays were used to survey nasal wash samples from 31 rehabilitating gopher tortoises. Mortality of tortoises significantly correlated with higher Helicobacter loads detected by qPCR (P = 0.028). Appropriate quarantine protocols for tortoises during rehabilitation should consider this organism. Upper respiratory disease in tortoises may involve complex microbial ecology; factors beyond Mycoplasmopsis (Mycoplasma) agassizii should be taken into account.
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Affiliation(s)
- Tasha M Desiderio
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Nicole I Stacy
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Robert J Ossiboff
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Marley Iredale
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Linda L Archer
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Amy B Alexander
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Darryl J Heard
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Sarah E Crevasse
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - William F Craft
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Daniel V E Fredholm
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Kyle A Donnelly
- Brevard Zoo and Sea Turtle Healing Center, Melbourne, FL, 32940, USA
| | - Justin F Rosenberg
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - April L Childress
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Kathy Russell
- Santa Fe College Teaching Zoo, Gainesville, FL, 32606, USA
| | - James F X Wellehan
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA.
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Trivellone V, Wei W, Filippin L, Dietrich CH. Screening potential insect vectors in a museum biorepository reveals undiscovered diversity of plant pathogens in natural areas. Ecol Evol 2021; 11:6493-6503. [PMID: 34141234 PMCID: PMC8207438 DOI: 10.1002/ece3.7502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/03/2022] Open
Abstract
Phytoplasmas (Mollicutes, Acholeplasmataceae), vector-borne obligate bacterial plant parasites, infect nearly 1,000 plant species and unknown numbers of insects, mainly leafhoppers (Hemiptera, Deltocephalinae), which play a key role in transmission and epidemiology. Although the plant-phytoplasma-insect association has been evolving for >300 million years, nearly all known phytoplasmas have been discovered as a result of the damage inflicted by phytoplasma diseases on crops. Few efforts have been made to study phytoplasmas occurring in noneconomically important plants in natural habitats. In this study, a subsample of leafhopper specimens preserved in a large museum biorepository was analyzed to unveil potential new associations. PCR screening for phytoplasmas performed on 227 phloem-feeding leafhoppers collected worldwide from natural habitats revealed the presence of 6 different previously unknown phytoplasma strains. This indicates that museum collections of herbivorous insects represent a rich and largely untapped resource for discovery of new plant pathogens, that natural areas worldwide harbor a diverse but largely undiscovered diversity of phytoplasmas and potential insect vectors, and that independent epidemiological cycles occur in such habitats, posing a potential threat of disease spillover into agricultural systems. Larger-scale future investigations will contribute to a better understanding of phytoplasma genetic diversity, insect host range, and insect-borne phytoplasma transmission and provide an early warning for the emergence of new phytoplasma diseases across global agroecosystems.
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Affiliation(s)
- Valeria Trivellone
- Illinois Natural History SurveyPrairie Research InstituteUniversity of IllinoisChampaignILUSA
| | - Wei Wei
- Molecular Plant Pathology LaboratoryBeltsville Agricultural Research CenterAgricultural Research ServiceUnited States Department of AgricultureBeltsvilleMDUSA
| | - Luisa Filippin
- CREA–VECouncil for Agricultural Research and EconomicsResearch Centre for Viticulture and EnologyConegliano, TrevisoItaly
| | - Christopher H. Dietrich
- Illinois Natural History SurveyPrairie Research InstituteUniversity of IllinoisChampaignILUSA
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Abstract
Ribosomal proteins (RPs) are highly conserved across the bacterial and archaeal domains. Although many RPs are essential for survival, genome analysis demonstrates the absence of some RP genes in many bacterial and archaeal genomes. Furthermore, global transposon mutagenesis and/or targeted deletion showed that elimination of some RP genes had only a moderate effect on the bacterial growth rate. Here, we systematically analyze the evolutionary conservation of RPs in prokaryotes by compiling the list of the ribosomal genes that are missing from one or more genomes in the recently updated version of the Clusters of Orthologous Genes (COG) database. Some of these absences occurred because the respective genes carried frameshifts, presumably, resulting from sequencing errors, while others were overlooked and not translated during genome annotation. Apart from these annotation errors, we identified multiple genuine losses of RP genes in a variety of bacteria and archaea. Some of these losses are clade-specific, whereas others occur in symbionts and parasites with dramatically reduced genomes. The lists of computationally and experimentally defined non-essential ribosomal genes show a substantial overlap, revealing a common trend in prokaryote ribosome evolution that could be linked to the architecture and assembly of the ribosomes. Thus, RPs that are located at the surface of the ribosome and/or are incorporated at a late stage of ribosome assembly are more likely to be non-essential and to be lost during microbial evolution, particularly, in the course of genome compaction.IMPORTANCEIn many prokaryote genomes, one or more ribosomal protein (RP) genes are missing. Analysis of 1,309 prokaryote genomes included in the COG database shows that only about half of the RPs are universally conserved in bacteria and archaea. In contrast, up to 16 other RPs are missing in some genomes, primarily, tiny (<1 Mb) genomes of host-associated bacteria and archaea. Ten universal and nine archaea-specific ribosomal proteins show clear patterns of lineage-specific gene loss. Most of the RPs that are frequently lost from bacterial genomes are located on the ribosome periphery and are non-essential in Escherichia coli and Bacillus subtilis These results reveal general trends and common constraints in the architecture and evolution of ribosomes in prokaryotes.
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Whole-Genome Sequence of the Mycoplasma ( Mesomycoplasma) hyorhinis DSM 25591 Type Strain. Microbiol Resour Announc 2021; 10:10/16/e00164-21. [PMID: 33888501 PMCID: PMC8063644 DOI: 10.1128/mra.00164-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The whole-genome sequence of the type strain Mycoplasma (“Mesomycoplasma”) hyorhinis DSM 25591 is reported and compared to the available sequences of the corresponding type strains from other strain collections to ascertain conformity. Knowledge of the identity of type strains is of importance for their application in standardized test systems. The whole-genome sequence of the type strain Mycoplasma (Mesomycoplasma) hyorhinis DSM 25591 is reported and compared to the available sequences of the corresponding type strains from other strain collections to ascertain conformity. Knowledge of the identity of type strains is of importance for their application in standardized test systems.
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Bozzi D, Rasmussen JA, Carøe C, Sveier H, Nordøy K, Gilbert MTP, Limborg MT. Salmon gut microbiota correlates with disease infection status: potential for monitoring health in farmed animals. Anim Microbiome 2021; 3:30. [PMID: 33879261 PMCID: PMC8056536 DOI: 10.1186/s42523-021-00096-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 04/04/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Infectious diseases cause significant production losses in aquaculture every year. Since the gut microbiota plays an essential role in regulating the host immune system, health and physiology, altered gut microbiota compositions are often associated with a diseased status. However, few studies have examined the association between disease severity and degree of gut dysbiosis, especially when the gut is not the site of the primary infection. Moreover, there is a lack of knowledge on whether bath treatment with formalin, a disinfectant commonly used in aquaculture to treat external infections, might affect the gut microbiome as a consequence of formalin ingestion. Here we investigate, through 16S rRNA gene metabarcoding, changes in the distal gut microbiota composition of a captive-reared cohort of 80 Atlantic salmon (Salmo salar L.), in consequence of an external bacterial skin infection due to a natural outbreak and subsequent formalin treatment. RESULTS We identified Tenacibaculum dicentrarchi as the causative disease pathogen and we show that the distal gut of diseased salmon presented a different composition from that of healthy individuals. A new, yet undescribed, Mycoplasma genus characterized the gut of healthy salmon, while in the sick fish we observed an increase in terms of relative abundance of Aliivibrio sp., a strain regarded as opportunistic. We also noticed a positive correlation between fish weight and Mycoplasma sp. relative abundance, potentially indicating a beneficial effect for its host. Moreover, we observed that the gut microbiota of fish treated with formalin was more similar to those of sick fish than healthy ones. CONCLUSIONS We conclude that external Tenacibaculum infections have the potential of indirectly affecting the host gut microbiota. As such, treatment optimization procedures should account for that. Formalin treatment is not an optimal solution from a holistic perspective, since we observe an altered gut microbiota in the treated fish. We suggest its coupling with a probiotic treatment aimed at re-establishing a healthy community. Lastly, we have observed a positive correlation of Mycoplasma sp. with salmon health and weight, therefore we encourage further investigations towards its potential utilization as a biomarker for monitoring health in salmon and potentially other farmed fish species.
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Affiliation(s)
- Davide Bozzi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark
| | - Jacob A Rasmussen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark
| | | | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark.
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Jenkins TP, Pritchard DI, Tanasescu R, Telford G, Papaiakovou M, Scotti R, Cortés A, Constantinescu CS, Cantacessi C. Experimental infection with the hookworm, Necator americanus, is associated with stable gut microbial diversity in human volunteers with relapsing multiple sclerosis. BMC Biol 2021; 19:74. [PMID: 33853585 PMCID: PMC8048248 DOI: 10.1186/s12915-021-01003-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/12/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Helminth-associated changes in gut microbiota composition have been hypothesised to contribute to the immune-suppressive properties of parasitic worms. Multiple sclerosis is an immune-mediated autoimmune disease of the central nervous system whose pathophysiology has been linked to imbalances in gut microbial communities. RESULTS In the present study, we investigated, for the first time, qualitative and quantitative changes in the faecal bacterial composition of human volunteers with remitting multiple sclerosis (RMS) prior to and following experimental infection with the human hookworm, Necator americanus (N+), and following anthelmintic treatment, and compared the findings with data obtained from a cohort of RMS patients subjected to placebo treatment (PBO). Bacterial 16S rRNA high-throughput sequencing data revealed significantly decreased alpha diversity in the faecal microbiota of PBO compared to N+ subjects over the course of the trial; additionally, we observed significant differences in the abundances of several bacterial taxa with putative immune-modulatory functions between study cohorts. Parabacteroides were significantly expanded in the faecal microbiota of N+ individuals for which no clinical and/or radiological relapses were recorded at the end of the trial. CONCLUSIONS Overall, our data lend support to the hypothesis of a contributory role of parasite-associated alterations in gut microbial composition to the immune-modulatory properties of hookworm parasites.
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Affiliation(s)
- Timothy P. Jenkins
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Present address: Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Radu Tanasescu
- Division of Clinical Neurology, School of Clinical Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, UK
| | - Gary Telford
- Department of Pharmacy, University of Nottingham, Nottingham, UK
| | - Marina Papaiakovou
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- National History Museum, London, UK
| | - Riccardo Scotti
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Alba Cortés
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Departament de Farmàcia i Tecnologia Farmacèutica i Parasitologia, Facultat de Farmàcia, Universitat de València, València, Spain
| | - Cris S. Constantinescu
- Division of Clinical Neurology, School of Clinical Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, UK
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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35
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The Changing Face of the Family Enterobacteriaceae (Order: " Enterobacterales"): New Members, Taxonomic Issues, Geographic Expansion, and New Diseases and Disease Syndromes. Clin Microbiol Rev 2021; 34:34/2/e00174-20. [PMID: 33627443 DOI: 10.1128/cmr.00174-20] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The family Enterobacteriaceae has undergone significant morphogenetic changes in its more than 85-year history, particularly during the past 2 decades (2000 to 2020). The development and introduction of new and novel molecular methods coupled with innovative laboratory techniques have led to many advances. We now know that the global range of enterobacteria is much more expansive than previously recognized, as they play important roles in the environment in vegetative processes and through widespread environmental distribution through insect vectors. In humans, many new species have been described, some associated with specific disease processes. Some established species are now observed in new infectious disease settings and syndromes. The results of molecular taxonomic and phylogenetics studies suggest that the current family Enterobacteriaceae should possibly be divided into seven or more separate families. The logarithmic explosion in the number of enterobacterial species described brings into question the relevancy, need, and mechanisms to potentially identify these taxa. This review covers the progression, transformation, and morphogenesis of the family from the seminal Centers for Disease Control and Prevention publication (J. J. Farmer III, B. R. Davis, F. W. Hickman-Brenner, A. McWhorter, et al., J Clin Microbiol 21:46-76, 1985, https://doi.org/10.1128/JCM.21.1.46-76.1985) to the present.
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36
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Munson E, Carroll KC. Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019. J Clin Microbiol 2021; 59:e01309-20. [PMID: 32967902 PMCID: PMC8111135 DOI: 10.1128/jcm.01309-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Millán J, Di Cataldo S, Volokhov DV, Becker DJ. Worldwide occurrence of haemoplasmas in wildlife: Insights into the patterns of infection, transmission, pathology and zoonotic potential. Transbound Emerg Dis 2020; 68:3236-3256. [PMID: 33210822 DOI: 10.1111/tbed.13932] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/13/2020] [Accepted: 11/14/2020] [Indexed: 12/17/2022]
Abstract
Haemotropic mycoplasmas (haemoplasmas) have increasingly attracted the attention of wildlife disease researchers due to a combination of wide host range, high prevalence and genetic diversity. A systematic review identified 75 articles that investigated haemoplasma infection in wildlife by molecular methods (chiefly targeting partial 16S rRNA gene sequences), which included 131 host genera across six orders. Studies were less common in the Eastern Hemisphere (especially Africa and Asia) and more frequent in the Artiodactyla and Carnivora. Meta-analysis showed that infection prevalence did not vary by geographic region nor host order, but wild hosts showed significantly higher prevalence than captive hosts. Using a taxonomically flexible machine learning algorithm, we also found vampire bats and cervids to have greater prevalence, whereas mink, a subclade of vesper bats, and true foxes all had lower prevalence compared to the remaining sampled mammal phylogeny. Haemoplasma genotype and nucleotide diversity varied little among wild mammals but were marginally lower in primates and bats. Coinfection with more than one haemoplasma species or genotype was always confirmed when assessed. Risk factors of infection identified were sociality, age, males and high trophic levels, and both prevalence and diversity were often higher in undisturbed environments. Haemoplasmas likely use different and concurrent transmission routes and typically display enzootic dynamics when wild populations are studied longitudinally. Haemoplasma pathology is poorly known in wildlife but appears subclinical. Candidatus Mycoplasma haematohominis, which causes disease in humans, probably has it natural host in bats. Haemoplasmas can serve as a model system in ecological and evolutionary studies, and future research on these pathogens in wildlife must focus on increasing the geographic range and taxa of studies and elucidating pathology, transmission and zoonotic potential. To facilitate such work, we recommend using universal PCR primers or NGS protocols to detect novel haemoplasmas and other genetic markers to differentiate among species and infer cross-species transmission.
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Affiliation(s)
- Javier Millán
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Zaragoza, Spain.,Fundación ARAID, Zaragoza, Spain.,Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Sophia Di Cataldo
- Programa de Doctorado en Medicina de la Conservación, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Dmitriy V Volokhov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, Oklahoma, USA
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Muratore M, Sun Y, Prather C. Environmental Nutrients Alter Bacterial and Fungal Gut Microbiomes in the Common Meadow Katydid, Orchelimum vulgare. Front Microbiol 2020; 11:557980. [PMID: 33193141 PMCID: PMC7645228 DOI: 10.3389/fmicb.2020.557980] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/30/2020] [Indexed: 11/13/2022] Open
Abstract
Insect gut microbiomes consist of bacteria, fungi, and viruses that can act as mutualists to influence the health and fitness of their hosts. While much has been done to increase understanding of the effects of environmental factors that drive insect ecology, there is less understanding of the effects of environmental factors on these gut microbial communities. For example, the effect of environmental nutrients on most insect gut microbiomes is poorly defined. To address this knowledge gap, we investigated the relationship between environmental nutrients and the gut microbial communities in a small study of katydids (n = 13) of the orthopteran species Orchelimum vulgare collected from a costal prairie system. We sampled O. vulgare from unfertilized plots, as well as from plots fertilized with added nitrogen and phosphorus or sodium separately and in combination. We found significantly higher Shannon diversity for the gut bacterial communities in O. vulgare from plots fertilized with added sodium as compared to those collected from plots without added sodium. In contrast, diversity was significantly lower in the gut fungal communities of grasshoppers collected from plots with added nitrogen and phosphorus, as well as those with added sodium, in comparison to those with no added nutrients. There was also a strong positive correlation between the gut bacterial and gut fungal community diversity within each sample. Indicator group analysis for added sodium plots included several taxa with known salt-tolerant bacterial and fungal representatives. Therefore, despite the small sample number, these results highlight the potential for the gut bacterial and fungal constituents to respond differently to changes in environmental nutrient levels. Future studies with a larger sample size will help identify mechanistic determinants driving these changes. Based on our findings and the potential contribution of gut microbes to insect fitness and function, consideration of abiotic factors like soil nutrients along with characteristic gut microbial groups is necessary for better understanding and conservation of this important insect herbivore.
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Affiliation(s)
- Melani Muratore
- Department of Biology, University of Dayton, Dayton, OH, United States
| | - Yvonne Sun
- Department of Biology, University of Dayton, Dayton, OH, United States
| | - Chelse Prather
- Department of Biology, University of Dayton, Dayton, OH, United States
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Zhang Y, Liang XF, He S, Chen X, Wang J, Li J, Zhu Q, Zhang Z, Li L, Alam MS. Effects of High Carbohydrate Diet-Modulated Microbiota on Gut Health in Chinese Perch. Front Microbiol 2020; 11:575102. [PMID: 33042089 PMCID: PMC7523390 DOI: 10.3389/fmicb.2020.575102] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022] Open
Abstract
High carbohydrate diet-induced damage in gut is linked to changes in gut permeability and microbiota. However, the mechanisms of action are not clear, especially in non-mammals. We performed the gut microbiota profiling in Chinese perch fed with different content of starch diets (0, 10, and 20%) by 16S rRNA sequencing. The gut permeability, metabolites, histological analysis, and inflammatory infiltration were evaluated. We found that gut microbial diversity, beneficial bacteria quantity, and lactic acid content were higher in C10 group than in the other groups. The lower level of gut microbial diversity was observed in C20 group, and mycoplasma was the overwhelmingly dominant species, but the butyric acid-producing bacteria and butyric acid level were significantly reduced. The gut permeability in C20 group was also increased due to the decreased mRNA expression levels of tight junction proteins caused by the butyric acid deficiency and gut lipid droplets accumulation. Then a large amount of LPS penetrated into the plasma, resulting in inflammation. These results suggested that high carbohydrate diet-induced damage in gut could be attributed to the endotoxemia, permeability, and gut microbiota, especially the role of mycoplasma and butyric acid-producing bacteria. In addition, predictive functional profiling of microbial communities by PICRUSt showed that C10 group enriched pathway related to membrane transport and down-regulated the pathways related to energy, coenzyme factor and vitamin metabolism, while C20 group exhibited reversed results. These data showed that the high-carbohydrate diet reversed the beneficial changes in gut microbial metabolism resulted from the medium-carbohydrate diet, and further demonstrated that microbiota played a key role in the gut damage caused by the high-carbohydrate diet. Our findings provide a reference for the targeted regulation of gut microbiota to mitigate the damage caused by the increase in starch content in fish feed (cost saving).
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Affiliation(s)
- Yanpeng Zhang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Shan He
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Xu Chen
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Jie Wang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Jiao Li
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Qiangsheng Zhu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Zhen Zhang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Lu Li
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Muhammad Shoaib Alam
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
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40
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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Cao Y, Trivellone V, Dietrich CH. A timetree for phytoplasmas (Mollicutes) with new insights on patterns of evolution and diversification. Mol Phylogenet Evol 2020; 149:106826. [PMID: 32283136 DOI: 10.1016/j.ympev.2020.106826] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/12/2020] [Accepted: 04/07/2020] [Indexed: 11/16/2022]
Abstract
The first comprehensive timetree is presented for phytoplasmas, a diverse group of obligate intracellular bacteria restricted to phloem sieve elements of vascular plants and tissues of their hemipteran insect vectors. Maximum likelihood-based phylogenetic analysis of DNA sequence data from the 16S rRNA and methionine aminopeptidase (map) genes yielded well resolved estimates of phylogenetic relationships among major phytoplasma lineages, 16Sr groups and known strains of phytoplasmas. Age estimates for divergences among two major lineages of Mollicutes based on a previous comprehensive bacterial timetree were used to calibrate an initial 16S timetree. A separate timetree was estimated based on the more rapidly-evolving map gene, with an internal calibration based on a recent divergence within two related 16Sr phytoplasma subgroups in group 16SrV thought to have been driven by the introduction of the North American leafhopper vector Scaphoideus titanus Ball into Europe during the early part of the 20th century. Combining the resulting divergence time estimates into a final 16S timetree suggests that evolutionary rates have remained relatively constant overall through the evolution of phytoplasmas and that the origin of this lineage, at ~641 million years ago (Ma), preceded the origin of land plants and hemipteran insects. Nevertheless, the crown group of phytoplasmas is estimated to have begun diversifying ~316 Ma, roughly coinciding with the origin of seed plants and Hemiptera. Some phytoplasma groups apparently associated with particular plant families or insect vector lineages generally arose more recently than their respective hosts and vectors, suggesting that vector-mediated host shifts have been an important mechanism in the evolutionary diversification of phytoplasmas. Further progress in understanding macroevolutionary patterns in phytoplasmas is hindered by large gaps in knowledge of the identity of competent vectors and lack of data on phytoplasma associations with non-economically important plants.
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Affiliation(s)
- Yanghui Cao
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA
| | - Valeria Trivellone
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA.
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA
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Janda JM. Proposed nomenclature or classification changes for bacteria of medical importance: taxonomic update 5. Diagn Microbiol Infect Dis 2020; 97:115047. [PMID: 32321664 DOI: 10.1016/j.diagmicrobio.2020.115047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/21/2020] [Accepted: 03/23/2020] [Indexed: 01/23/2023]
Abstract
A key aspect of medical, public health, and diagnostic microbiology laboratories is the accurate identification and rapid reporting and communication to medical staff regarding patients with infectious agents of clinical importance. Microbial taxonomy continues to change at a very rapid rate in the era of molecular diagnostics including whole genome sequencing. This update focuses on taxonomic changes and proposals that may be of medical importance from 2018 to 2020.
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Affiliation(s)
- J Michael Janda
- Public Health Laboratory, Public Health Services Department, Kern County, Bakersfield, CA 93306-3302.
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Gupta RS, Oren A. Necessity and rationale for the proposed name changes in the classification of Mollicutes species. Reply to: 'Recommended rejection of the names Malacoplasma gen. nov., Mesomycoplasma gen. nov., Metamycoplasma gen. nov., Metamycoplasmataceae fam. nov., Mycoplasmoidaceae fam. nov., Mycoplasmoidales ord. nov., Mycoplasmoides gen. nov., Mycoplasmopsis gen. nov. [Gupta, Sawnani, Adeolu, Alnajar and Oren 2018] and all proposed species comb. nov. placed therein', by M. Balish et al. ( Int J Syst Evol Microbiol, 2019;69:3650-3653). Int J Syst Evol Microbiol 2020; 70:1431-1438. [PMID: 31971499 DOI: 10.1099/ijsem.0.003869] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
This response summarizes the highly disordered state of the Mollicutes taxonomy that existed until recently, where most Mollicutes taxa lacked proper circumscriptions and their names were not in accordance with the International Code of Nomenclature of Prokaryotes and illegitimate. We also summarize the comprehensive phylogenomic and comparative genomic studies forming the basis for the proposed changes in the classification of Mollicultes species. Our responses to the concerns raised by Balish et al., show that the proposed taxonomic changes do not violate any essential point of the Code. Instead the proposed name changes rectify numerous taxonomic anomalies that have long plagued the classification of Mollicutes species, leading to a better understanding of their evolutionary relationships and bringing their nomenclature in conformity with the Code.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
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Muratore M, Prather C, Sun Y. The gut bacterial communities across six grasshopper species from a coastal tallgrass prairie. PLoS One 2020; 15:e0228406. [PMID: 31999781 PMCID: PMC6992175 DOI: 10.1371/journal.pone.0228406] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Insect microbiomes play an important role in the health and fitness of insect hosts by contributing to nutrient absorption, immune health, and overall ecological fitness. As such, research interests in insect microbiomes have focused on agriculturally and industrially important organisms such as honey bees and termites. Orthopterans, on the other hand, have not been well explored for their resident microbial communities. Grasshoppers are an integral part of grassland ecosystems and provide important ecosystem services. Conversely, grasshoppers can be an agricultural pest requiring management with broad spectrum pesticides. However, little is known about the microbiomes of grasshoppers and their potential contribution to grasshopper biology. Here we examine the gut microbiome of six species of grasshoppers (n = 60) from a coastal tallgrass prairie ecosystem to gain a better understanding of the microbial communities present across the orthopteran order in this ecosystem. We found that there are bacterial phyla common to all six grasshopper species: Actinobacteria, Proteobacteria, Firmicutes, and to a lesser degree, Tenericutes. Although the grasshopper species shared a high relative abundance of these groups, there were notable shifts in dominant phyla depending on the grasshopper species. Moreover, measures of alpha diversity revealed a more diverse microbiome in males than females. Our observations support the hypothesis that there is a "core" group of bacterial families in these grasshopper species and factors such as trophic behaviors and the evolution of the host may contribute to the shifts in prevalence among these core microbial groups.
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Affiliation(s)
- Melani Muratore
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
| | - Chelse Prather
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
| | - Yvonne Sun
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
- * E-mail:
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Spergser J, Botes A, Nel T, Ruppitsch W, Lepuschitz S, Langer S, Ries S, Dinhopl N, Szostak M, Loncaric I, Busse HJ. Mycoplasma nasistruthionis sp. nov. and Mycoplasma struthionis sp. nov. isolated from ostriches with respiratory disease. Syst Appl Microbiol 2019; 43:126047. [PMID: 31859015 DOI: 10.1016/j.syapm.2019.126047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 12/11/2022]
Abstract
Twelve Mycoplasma (M.) strains isolated from the nose, the trachea, and the lung of ostriches (Struthio camelus) displaying respiratory disease were investigated. Analysis of 16S rRNA gene sequences placed five of these strains within the M. synoviae cluster, and seven strains within the M. hominis cluster of genus Mycoplasma, which was further confirmed by analyses of the 16S-23S rRNA intergenic spacer region, and partial rpoB gene and amino acid sequences. Genomic information as well as phenotypic features obtained by matrix-assisted laser desorption ionization time of flight (MALDI-ToF) mass spectrometry analysis and serological reactions indicated that the strains examined are representatives of two hitherto unclassified species of genus Mycoplasma, for which the names Mycoplasma nasistruthionis sp. nov., with type strain 2F1AT (= ATCC BAA-1893T = DSM 22456T), and Mycoplasma struthionis sp. nov., with type strain 237IAT (= ATCC BAA-1890T = DSM 22453T), are proposed.
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Affiliation(s)
- Joachim Spergser
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria.
| | - Annelise Botes
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Tyron Nel
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Sarah Lepuschitz
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Stefan Langer
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Sally Ries
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Nora Dinhopl
- Institute of Pathology, University of Veterinary Medicine, Vienna, Austria
| | - Michael Szostak
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Hans-Jürgen Busse
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
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Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Is a Superior Diagnostic Tool for the Identification and Differentiation of Mycoplasmas Isolated from Animals. J Clin Microbiol 2019; 57:JCM.00316-19. [PMID: 31217275 DOI: 10.1128/jcm.00316-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/14/2019] [Indexed: 11/20/2022] Open
Abstract
In veterinary diagnostic laboratories, identification of mycoplasmas is achieved by demanding, cost-intensive, and time-consuming methods that rely on antigenic or genetic identification. Since matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) seems to represent a promising alternative to the currently practiced cumbersome diagnostics, we assessed its applicability for the identification of almost all mycoplasma species isolated from vertebrate animals so far. For generating main spectrum profiles (MSPs), the type strains of 98 Mycoplasma, 11 Acholeplasma, and 5 Ureaplasma species and, in the case of 69 species, 1 to 7 clinical isolates were used. To complete the database, 3 to 7 representatives of 23 undescribed Mycoplasma species isolated from livestock, companion animals, and wildlife were also analyzed. A large in-house library containing 530 MSPs was generated, and the diversity of spectra within a species was assessed by constructing dendrograms based on a similarity matrix. All strains of a given species formed cohesive clusters clearly distinct from all other species. In addition, phylogenetically closely related species also clustered closely but were separated accurately, indicating that the established database was highly robust, reproducible, and reliable. Further validation of the in-house mycoplasma library using 335 independent clinical isolates of 32 mycoplasma species confirmed the robustness of the established database by achieving reliable species identification with log scores of ≥1.80. In summary, MALDI-TOF MS proved to be an excellent method for the identification and differentiation of animal mycoplasmas, combining convenience, ease, speed, precision, and low running costs. Furthermore, this method is a powerful and supportive tool for the taxonomic resolution of animal mycoplasmas.
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Ramírez AS, Vega-Orellana OM, Viver T, Poveda JB, Rosales RS, Poveda CG, Spergser J, Szostak MP, Caballero MJ, Ressel L, Bradbury JM, Mar Tavío M, Karthikeyan S, Amann R, Konstantinidis KT, Rossello-Mora R. First description of two moderately halophilic and psychrotolerant Mycoplasma species isolated from cephalopods and proposal of Mycoplasma marinum sp. nov. and Mycoplasma todarodis sp. nov. Syst Appl Microbiol 2019; 42:457-467. [PMID: 31072660 DOI: 10.1016/j.syapm.2019.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/05/2019] [Accepted: 04/05/2019] [Indexed: 11/29/2022]
Abstract
Two moderately halophilic and psychrotolerant new Mycoplasma species were isolated from common cephalopods. Three strains were isolated in pure culture from two individual European flying squid (Todarodes sagittatus), and two individual octopuses (Octopus vulgaris). The strains showed optimal growth at 25 °C and a salinity of 3% (w/v) NaCl. Molecular analyses revealed that the isolates belonged to two new, but phylogenetically related species, divergent from all previously described Mollicutes, representing the first marine isolates of the class, and also the first Mycoplasma strains for which NaCl requirement has been demonstrated. A genome search against all available marine metagenomes and 16S rRNA gene databases indicated that these two species represent a novel non-free-living marine lineage of Mollicutes, specifically associated with marine animals. Morphology and physiology were compatible with other members of this group, and genomic and phenotypic analyses demonstrated that these organisms represent two novel species of the genus Mycoplasma, for which the names Mycoplasma marinum sp. nov. and Mycoplasma todarodis sp. nov. are proposed; the type strains are PET (DSM 105487T, CIP 111404T) and 5HT (DSM 105,488T, CIP 111405T), respectively.
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Affiliation(s)
- Ana S Ramírez
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Orestes M Vega-Orellana
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), 07190, Esporles, Spain
| | - José B Poveda
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain.
| | - Rubén S Rosales
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Carlos G Poveda
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Joachim Spergser
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Michael P Szostak
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Mª José Caballero
- Unidad de Histología y Patología Animal, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Lorenzo Ressel
- University of Liverpool, Institute of Veterinary Science, Leahurst Campus, Neston CH64 7TE, UK
| | - Janet M Bradbury
- University of Liverpool, Institute of Veterinary Science, Leahurst Campus, Neston CH64 7TE, UK
| | - Mª Mar Tavío
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Smruthi Karthikeyan
- School of Civil & Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rudolf Amann
- Department of Molecular Ecology, Max-Planck-Institut für Marine Mikrobiologie, Bremen D-28359, Germany
| | - Konstantinos T Konstantinidis
- School of Civil & Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), 07190, Esporles, Spain
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Clarke LJ, Suter L, King R, Bissett A, Deagle BE. Antarctic Krill Are Reservoirs for Distinct Southern Ocean Microbial Communities. Front Microbiol 2019; 9:3226. [PMID: 30697197 PMCID: PMC6340936 DOI: 10.3389/fmicb.2018.03226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/11/2018] [Indexed: 11/13/2022] Open
Abstract
Host-associated bacterial communities have received limited attention in polar habitats, but are likely to represent distinct nutrient-rich niches compared to the surrounding environment. Antarctic krill (Euphausia superba) are a super-abundant species with a circumpolar distribution, and the krill microbiome may make a substantial contribution to marine bacterial diversity in the Southern Ocean. We used high-throughput sequencing of the bacterial 16S ribosomal RNA gene to characterize bacterial diversity in seawater and krill tissue samples from four locations south of the Kerguelen Plateau, one of the most productive regions in the Indian Sector of the Southern Ocean. Krill-associated bacterial communities were distinct from those of the surrounding seawater, with different communities inhabiting the moults, digestive tract and faecal pellets, including several phyla not detected in the surrounding seawater. Digestive tissues from many individuals contained a potential gut symbiont (order: Mycoplasmoidales) shown to improve survival on a low quality diet in other crustaceans. Antarctic krill swarms thus influence Southern Ocean microbial communities not only through top-down grazing of eukaryotic cells and release of nutrients into the water column, but also by transporting distinct microbial assemblages horizontally via migration and vertically via sinking faecal pellets and moulted exuviae. Changes to Antarctic krill demographics or distribution through fishing pressure or climate-induced range shifts will also influence the composition and dispersal of Southern Ocean microbial communities.
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Affiliation(s)
- Laurence J Clarke
- Antarctic Climate and Ecosystems Cooperative Research Centre, University of Tasmania, Hobart, TAS, Australia
| | - Léonie Suter
- Australian Antarctic Division, Kingston, TAS, Australia
| | - Robert King
- Australian Antarctic Division, Kingston, TAS, Australia
| | - Andrew Bissett
- Commonwealth Scientific and Industrial Research Organisation, Hobart, TAS, Australia
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49
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Oren A, Garrity GM. Notification of changes in taxonomic opinion previously published outside the IJSEM. Int J Syst Evol Microbiol 2019; 69:13-32. [PMID: 30614782 DOI: 10.1099/ijsem.0.003171] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Aharon Oren
- 1The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- 2Department of Microbiology and Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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A phylogenomic and molecular markers based taxonomic framework for members of the order Entomoplasmatales: proposal for an emended order Mycoplasmatales containing the family Spiroplasmataceae and emended family Mycoplasmataceae comprised of six genera. Antonie van Leeuwenhoek 2018; 112:561-588. [PMID: 30392177 DOI: 10.1007/s10482-018-1188-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/14/2018] [Indexed: 01/01/2023]
Abstract
The "Spiroplasma cluster" is a taxonomically heterogeneous assemblage within the phylum Tenericutes encompassing different Entomoplasmatales species as well as the genus Mycoplasma, type genus of the order Mycoplasmatales. Within this cluster, the family Entomoplasmataceae contains two non-cohesive genera Entomoplasma and Mesoplasma with their members exhibiting extensive polyphyletic branching; additionally, the genus Mycoplasma is also embedded within this family. Genome sequences are now available for all 19 Entomoplasmataceae species with validly published names, as well as 6 of the 7 species from the genus Mycoplasma. With the aim of developing a reliable phylogenetic and taxonomic framework for the family Entomoplasmataceae, exhaustive phylogenetic and comparative genomic studies were carried out on these genome sequences. Phylogenetic trees were constructed based on concatenated sequences of 121 core proteins for this cluster, 67 conserved proteins shared with the phylum Firmicutes, 40 ribosomal proteins, three major subunits of RNA polymerase (RpoA, B and C) by different means and also for the 16S rRNA gene sequences. The interspecies relationships as well as different species groups observed in these trees were identical and robustly resolved. In all of these trees, members of the genera Mesoplasma and Entomoplasma formed three and two distinct clades, respectively, which were interspersed among the members of the other genus. The observed species groupings in the phylogenetic trees are independently strongly supported by our identification of 103 novel molecular markers or synapomorphies in the forms of conserved signature indels and conserved signature proteins, which are uniquely shared by the members of different observed species clades. To account for the different observed species clades, we are proposing a division of the genus Mesoplasma into an emended genus Mesoplasma and two new genera Tullyiplasma gen. nov. and Edwardiiplasma gen. nov. Likewise, to recognize the distinct species groupings of Entomoplasma, we are proposing its division into an emended genus Entomoplasma and a new genus Williamsoniiplasma gen. nov. Lastly, to rectify the long-existing taxonomic anomaly caused by the presence of genus Mycoplasma (order Mycoplasmatales) within the Entomoplasmatales, we are proposing an emendation of the family Mycoplasmataceae to include both Entomoplasmataceae plus Mycoplasma species and an emendation of the order Mycoplasmatales, which now comprises of the emended family Mycoplasmataceae and the family Spiroplasmataceae. The taxonomic reclassifications proposed here accurately reflect the species relationships within this group of Tenericutes and they should lead to a better understanding of their biological and pathogenic characteristics.
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